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This page was generated on 2015-10-27 17:38:29 -0400 (Tue, 27 Oct 2015).
| Package 813/1104 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| puma 3.12.0 Xuejun Liu
| linux1.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK |  | |||||
| windows1.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | | |||||
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK | | |||||
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ OK ] | OK | |
| Package: puma |
| Version: 3.12.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings puma_3.12.0.tar.gz |
| StartedAt: 2015-10-27 06:48:05 -0400 (Tue, 27 Oct 2015) |
| EndedAt: 2015-10-27 06:54:32 -0400 (Tue, 27 Oct 2015) |
| EllapsedTime: 386.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: puma.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings puma_3.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/puma.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘puma/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘puma’ version ‘3.12.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘puma’ can be installed ... [20s/20s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘oligoClasses’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
‘ROCR’ ‘limma’ ‘pumadata’ ‘snow’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
':::' calls which should be '::':
‘affy:::mm’ ‘affy:::pm’ ‘affy:::probeNames’ ‘oligo:::mm’ ‘oligo:::pm’
‘oligo:::probeNames’ ‘oligo:::rma’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
PMmmgmos: no visible global function definition for ‘description’
calcAUC: no visible global function definition for ‘prediction’
calcAUC: no visible global function definition for ‘performance’
calculateLimma: no visible global function definition for ‘lmFit’
calculateLimma: no visible global function definition for
‘contrasts.fit’
calculateLimma: no visible global function definition for ‘eBayes’
clusterApplyLBDots : submit: no visible global function definition for
‘sendCall’
clusterApplyLBDots: no visible global function definition for
‘recvOneResult’
compareLimmapumaDE: no visible global function definition for
‘vennDiagram’
gmhta: no visible global function definition for ‘clusterEvalQ’
gmhta: no visible global function definition for ‘clusterApplyLB’
gmhta: no visible global function definition for ‘stopCluster’
gmoExon: no visible global function definition for ‘clusterEvalQ’
gmoExon: no visible global function definition for ‘clusterApplyLB’
gmoExon: no visible global function definition for ‘stopCluster’
igmoExon: no visible global function definition for ‘clusterEvalQ’
igmoExon: no visible global function definition for ‘clusterApplyLB’
igmoExon: no visible global function definition for ‘stopCluster’
plotErrorBars: no visible global function definition for ‘even’
plotErrorBars: no visible global function definition for ‘odd’
plotROC: no visible global function definition for ‘prediction’
plotROC: no visible global function definition for ‘performance’
pumaComb: no visible global function definition for ‘getMPIcluster’
pumaComb: no visible global function definition for ‘makeCluster’
pumaComb: no visible global function definition for ‘clusterEvalQ’
pumaComb: no visible global function definition for ‘clusterApplyLB’
pumaCombImproved: no visible global function definition for
‘getMPIcluster’
pumaCombImproved: no visible global function definition for
‘makeCluster’
pumaCombImproved: no visible global function definition for
‘clusterEvalQ’
pumaCombImproved: no visible global function definition for
‘clusterApplyLB’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [217s/217s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
puma-package 45.269 2.429 47.751
hcomb 33.283 3.500 36.820
pumaDE 30.143 1.795 31.966
pumaCombImproved 18.396 1.611 20.024
pumaClustii 17.299 0.147 17.463
DEResult-class 11.721 0.428 12.158
pumaComb 11.455 0.380 11.846
pumaPCA 8.260 0.160 8.424
plot-methods 8.087 0.125 8.218
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.2-bioc/meat/puma.Rcheck/00check.log’
for details.
puma.Rcheck/00install.out:
* installing *source* package ‘puma’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c PMmultimgmos.c -o PMmultimgmos.o
PMmultimgmos.c:425:23: warning: unused variable 'j' [-Wunused-variable]
static IINTEGER i,j;
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c cregistration.c -o cregistration.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c donlp2.c -o donlp2.o
donlp2.c:270:5: warning: '/*' within block comment [-Wcomment]
/* bloc */
^
donlp2.c:471:39: warning: unused variable 'gxi' [-Wunused-variable]
static DDOUBLE tol1 ,bd0,infiny,gxi,hxi,term;
^
donlp2.c:470:26: warning: unused variable 'k' [-Wunused-variable]
static IINTEGER i,j,k;
^
donlp2.c:471:28: warning: unused variable 'bd0' [-Wunused-variable]
static DDOUBLE tol1 ,bd0,infiny,gxi,hxi,term;
^
donlp2.c:471:43: warning: unused variable 'hxi' [-Wunused-variable]
static DDOUBLE tol1 ,bd0,infiny,gxi,hxi,term;
^
donlp2.c:2034:1: warning: '/*' within block comment [-Wcomment]
/* **************************************************************************** */
^
donlp2.c:2707:1: warning: '/*' within block comment [-Wcomment]
/* inactive
^
donlp2.c:2090:21: warning: unused variable 'eval_err' [-Wunused-variable]
static LLOGICAL eval_err;
^
donlp2.c:2076:22: warning: unused variable 'l' [-Wunused-variable]
static IINTEGER l,l0,i,j,k,csssig,csirup,csreg,cschgx;
^
donlp2.c:4123:27: warning: unused variable 'term1' [-Wunused-variable]
static DDOUBLE term,term1;
^
donlp2.c:4127:5: warning: unused label 'L100' [-Wunused-label]
L100:
^˜˜˜˜
donlp2.c:4412:24: warning: unused variable 'j' [-Wunused-variable]
static IINTEGER i,j;
^
donlp2.c:5027:28: warning: unused variable 'l' [-Wunused-variable]
static IINTEGER i,j,k,l,i1,icur,ipiv;
^
donlp2.c:6418:9: warning: unused label 'L500' [-Wunused-label]
L500:
^˜˜˜˜
donlp2.c:5755:48: warning: unused variable 'term2' [-Wunused-variable]
su1,su2,condr,infiny,term1,term2,
^
donlp2.c:7153:5: warning: unused label 'L20' [-Wunused-label]
L20:
^˜˜˜
donlp2.c:7878:16: warning: unused variable 'j' [-Wunused-variable]
IINTEGER i,j;
^
donlp2.c:7916:14: warning: unused variable 'i' [-Wunused-variable]
IINTEGER i;
^
donlp2.c:8009:16: warning: unused variable 'j' [-Wunused-variable]
IINTEGER i,j;
^
donlp2.c:8044:14: warning: unused variable 'i' [-Wunused-variable]
IINTEGER i;
^
donlp2.c:8141:16: warning: unused variable 'j' [-Wunused-variable]
IINTEGER i,j;
^
donlp2.c:8177:14: warning: unused variable 'i' [-Wunused-variable]
IINTEGER i;
^
22 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c gme.c -o gme.o
gme.c:268:6: warning: unused variable 'finishflag' [-Wunused-variable]
int finishflag = 1;
^
gme.c:265:6: warning: unused variable 'niter' [-Wunused-variable]
int niter = 1, nx;
^
gme.c:354:9: warning: unused variable 'xxx' [-Wunused-variable]
int xxx=(2+in_param->num_prctile)*in_param->numofgenes*in_param->chips;
^
gme.c:349:23: warning: unused variable 'alpha_temp' [-Wunused-variable]
double alphai, c, d,alpha_temp,kk_gene;
^
gme.c:349:10: warning: unused variable 'alphai' [-Wunused-variable]
double alphai, c, d,alpha_temp,kk_gene;
^
gme.c:347:15: warning: unused variable 'k' [-Wunused-variable]
int p, i, j, k, q,px,cal_j,cal_i,cal_index,temp_i,temp_j,maph_i,mal,mb_x,t,mm,mut_x,mut_y,index;
^
gme.c:347:18: warning: unused variable 'q' [-Wunused-variable]
int p, i, j, k, q,px,cal_j,cal_i,cal_index,temp_i,temp_j,maph_i,mal,mb_x,t,mm,mut_x,mut_y,index;
^
gme.c:347:20: warning: unused variable 'px' [-Wunused-variable]
int p, i, j, k, q,px,cal_j,cal_i,cal_index,temp_i,temp_j,maph_i,mal,mb_x,t,mm,mut_x,mut_y,index;
^
gme.c:894:10: warning: unused variable 'res_isoform' [-Wunused-variable]
SEXP res_isoform=NULL;
^
gme.c:897:11: warning: unused variable 't' [-Wunused-variable]
int i, j,t,t1;
^
gme.c:897:13: warning: unused variable 't1' [-Wunused-variable]
int i, j,t,t1;
^
11 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c ipplr_c.c -o ipplr_c.o
ipplr_c.c:255:114: warning: '&&' within '||' [-Wlogical-op-parentheses]
while(fmaxn_ipplr(diff_mu1,in_param.conds)>in_param.eps||fmaxn_ipplr(diff_lamda,in_param.conds)>in_param.eps&&n<2000)
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
ipplr_c.c:255:114: note: place parentheses around the '&&' expression to silence this warning
while(fmaxn_ipplr(diff_mu1,in_param.conds)>in_param.eps||fmaxn_ipplr(diff_lamda,in_param.conds)>in_param.eps&&n<2000)
^
( )
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c multimgmos.c -o multimgmos.o
multimgmos.c:264:8: warning: unused variable 'Rf_pf' [-Wunused-variable]
FILE *pf=NULL;
^
/Library/Frameworks/R.framework/Resources/include/Rmath.h:272:13: note: expanded from macro 'pf'
#define pf Rf_pf
^
multimgmos.c:660:23: warning: unused variable 'j' [-Wunused-variable]
static IINTEGER i,j;
^
multimgmos.c:773:9: warning: unused variable 's5' [-Wunused-variable]
double s5[MAX_NUM_PROBE]={0.0};
^
multimgmos.c:893:95: warning: suggest braces around initialization of subobject [-Wmissing-braces]
double alphaii[MAX_NUM_COND]={0.0}, s1[MAX_NUM_COND]={0.0}, s2[MAX_NUM_PROBE][MAX_NUM_COND]={0.0}, c, d_mmgmos, t1, s3, s4;
^˜˜
{ }
4 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c newx.c -o newx.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pplr_c.c -o pplr_c.o
pplr_c.c:185:65: warning: unused variable 'x_temp' [-Wunused-variable]
double exp_c[MAX_NUM_REPLICATE], var_c[MAX_NUM_REPLICATE], x_temp[MAX_NUM_COND];
^
pplr_c.c:444:35: warning: unused variable 'lam_temp' [-Wunused-variable]
double mu_temp[MAX_NUM_COND], lam_temp[MAX_NUM_COND];
^
pplr_c.c:444:12: warning: unused variable 'mu_temp' [-Wunused-variable]
double mu_temp[MAX_NUM_COND], lam_temp[MAX_NUM_COND];
^
pplr_c.c:442:38: warning: unused variable 'var_c' [-Wunused-variable]
double exp_c[MAX_NUM_REPLICATE], var_c[MAX_NUM_REPLICATE], x_temp[MAX_NUM_COND];
^
4 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pumaclust_c.c -o pumaclust_c.o
pumaclust_c.c:384:41: warning: unused variable 'var_temp' [-Wunused-variable]
double t1, t2, **mujd=NULL, expr_temp, var_temp;
^
pumaclust_c.c:384:13: warning: unused variable 't2' [-Wunused-variable]
double t1, t2, **mujd=NULL, expr_temp, var_temp;
^
pumaclust_c.c:384:30: warning: unused variable 'expr_temp' [-Wunused-variable]
double t1, t2, **mujd=NULL, expr_temp, var_temp;
^
pumaclust_c.c:384:9: warning: unused variable 't1' [-Wunused-variable]
double t1, t2, **mujd=NULL, expr_temp, var_temp;
^
4 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c pumaclustii_c.c -o pumaclustii_c.o
pumaclustii_c.c:972:21: warning: unused variable 'j' [-Wunused-variable]
static IINTEGER j;
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c user_eval.c -o user_eval.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o puma.so PMmultimgmos.o cregistration.o donlp2.o gme.o ipplr_c.o multimgmos.o newx.o pplr_c.o pumaclust_c.o pumaclustii_c.o user_eval.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-bioc/meat/puma.Rcheck/puma/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (puma)
puma.Rcheck/puma-Ex.timings:
| name | user | system | elapsed | |
| DEResult-class | 11.721 | 0.428 | 12.158 | |
| PMmmgmos | 0.001 | 0.000 | 0.001 | |
| bcomb | 0.247 | 0.020 | 0.267 | |
| calcAUC | 0.127 | 0.012 | 0.153 | |
| calculateFC | 3.565 | 0.081 | 3.649 | |
| calculateLimma | 2.793 | 0.052 | 2.847 | |
| calculateTtest | 0.157 | 0.001 | 0.159 | |
| clusterNormE | 0.066 | 0.003 | 0.070 | |
| clusterNormVar | 0.059 | 0.006 | 0.064 | |
| createContrastMatrix | 2.061 | 0.045 | 2.106 | |
| createDesignMatrix | 1.782 | 0.020 | 1.804 | |
| erfc | 0.001 | 0.001 | 0.000 | |
| exprReslt-class | 1.083 | 0.037 | 1.122 | |
| gmhta | 0.001 | 0.000 | 0.001 | |
| gmoExon | 0.001 | 0.000 | 0.001 | |
| hcomb | 33.283 | 3.500 | 36.820 | |
| igmoExon | 0.000 | 0.001 | 0.000 | |
| legend2 | 0.004 | 0.000 | 0.005 | |
| license.puma | 0.002 | 0.001 | 0.002 | |
| matrixDistance | 0.001 | 0.000 | 0.001 | |
| mgmos | 0.000 | 0.000 | 0.001 | |
| mmgmos | 0 | 0 | 0 | |
| normalisation.gs | 0.013 | 0.004 | 0.017 | |
| numFP | 0.003 | 0.001 | 0.003 | |
| numOfFactorsToUse | 0.309 | 0.008 | 0.316 | |
| numTP | 0.008 | 0.000 | 0.008 | |
| orig_pplr | 0.221 | 0.008 | 0.229 | |
| plot-methods | 8.087 | 0.125 | 8.218 | |
| plotErrorBars | 0.373 | 0.011 | 0.385 | |
| plotHistTwoClasses | 0.013 | 0.000 | 0.014 | |
| plotROC | 0.110 | 0.002 | 0.112 | |
| pplr | 0.223 | 0.038 | 0.260 | |
| puma-package | 45.269 | 2.429 | 47.751 | |
| pumaClustii | 17.299 | 0.147 | 17.463 | |
| pumaComb | 11.455 | 0.380 | 11.846 | |
| pumaCombImproved | 18.396 | 1.611 | 20.024 | |
| pumaDE | 30.143 | 1.795 | 31.966 | |
| pumaFull | 0.001 | 0.001 | 0.001 | |
| pumaNormalize | 0.420 | 0.017 | 0.438 | |
| pumaPCA | 8.260 | 0.160 | 8.424 | |
| pumaclust | 1.544 | 0.020 | 1.566 | |
| removeUninformativeFactors | 0.077 | 0.003 | 0.081 | |